Cytochrome unfolding pathways from computational analysis of crystal structures

• We probed the geometrical factors that influence early unfolding in cytochromes.
• Cytochromes c, c′ and c-b562 were our models.
• This permits prediction of unfolding propensities from known structures.

We have developed a model to study the role of geometrical factors in influencing the early stages of unfolding in three cytochromes: cyt c′, cyt c-b562 and cyt c  . Each stage in unfolding is quantified by the spatial extension λ̂i of n-residue segments, and by their angular extension 〈βn〉. Similarities and differences between and among the three cytochromes in the unfolding of helical and non-helical regions can be determined by analyzing the data for each signature separately. Definite conclusions can be drawn when spatial and angular changes are considered in tandem. To facilitate comparisons, we present graphical portraits of the three cytochromes at the same stage of unfolding, and in relation to their native state structures. We also display specific segments at different stages of unfolding to illustrate differences in stability of defined domains thereby allowing us to make specific predictions on the unfolding of corresponding internal and terminal helices in cyt c′ and cyt c-b562. Our work accords with an earlier experimental report on the presence and persistence of a hydrophobic core in cyt c.

Native (goldenrod) and second extended state for cyt c. The N-terminal and C-terminal α-helices are in blue, the green loop and the green α-helix are in green, the infrared loop is in magenta, and the red loop in red.Figure optionsDownload as PowerPoint slide